R/queries.R
In MilesMcBain/deplearning: Analyse Dependencies of R Code
#' Check R source dependencies.
#'
#' `depl_check` analyses R source for dependency references:
#' `library(<package>)`, `require(<package>)`, `<package>::func`,
#' `pload(<package>, <package>)`. The dependencies are then located in either the
#' local library, CRAN, or GitHub. Installed versions are compared with repository versions,
#' with CRAN taking precendence over GitHub (Even if a local package was installed from GitHub).
#'
#' A report is output to the console containing information about missing and out of date dependencies.
#' If there are any missing or out of date, a prompt is made to automatically update and install dependencies.
#'
#' @param source_path a file or directory path.
#'
#' @return A list of dataframes containing package metadata. Convenient for diagnostics or further processing.
#' @export
#'
#' @examples
#' \dontrun{
#' depl_check("~/repos/my_analysis")
#' depl_check("./report.Rmd")
#' }
#'
depl_check <- function(source_path = "."){
stopifnot(is.character(source_path))
cat("[deplearning] Starting dependency check.\n")
if(is_R_file(source_path)){
cat("[deplearning] Scanning file", source_path)
doc <- readLines(con = source_path)
lib_list <- find_doc_libs(doc)
}else{
cat("[deplearning] Searching path", source_path, "\n")
R_files <- dir(".", pattern = "\\.(rmd|r)$" , recursive = TRUE, ignore.case = TRUE)
if(length(R_files > 0)){
cat("[deplearning] Scanning", length(R_files), "R source files...")
lib_list <-
purrr::map(R_files, readLines) %>%
purrr::map(find_doc_libs) %>%
unlist() %>%
unique()
}else{
cat("[deplearning] Did not find any R source files in", source_path, ".\n")
return()
}
}
cat(" done.\n")
depl_check_run(lib_list)
}
#' Check R dependencies in the currently active Rstudio pane.
#'
#' See `depl_check()` for details.
#'
#' @return A list of dataframes containing package metadata. Convenient for diagnostics or further processing.
#' @export
depl_check_addin <- function(){
cat("[deplearning] Starting check run.\n")
cat("[deplearning] Scanning RStudio pane...")
lib_list <- find_doc_libs(rstudioapi::getActiveDocumentContext()$contents)
cat(" done.\n")
depl_check_run(lib_list)
}
# Subfunctuion of depl_check to allow the same body to be used for RStudio addin
# and file path version.
depl_check_run <- function(lib_list){
if(length(lib_list) == 0){
cat("[deplearning] found no dependencies in this code.\n")
return()
}
#remove base packages if present
lib_list <- lib_list[!lib_list %in% c("base","tools","utils")]
cat(sprintf("[deplearning] Found %i dependencies.\n", length(lib_list)))
pkg_install_status <-
tibble::tibble(
package = lib_list,
installed = are_installed(lib_list)
)
cat("[deplearning] Fetching remote data...")
installed_pkg_df <- get_installed_data(pkg_install_status)
n_behind_CRAN <- sum(installed_pkg_df$CRAN_up_to_date == -1, na.rm = TRUE)
n_behind_GH <- sum(installed_pkg_df$GH_up_to_date == -1, na.rm = TRUE)
n_missing <- sum(!pkg_install_status$installed)
n_uptodate_installed <-
sum(installed_pkg_df$CRAN_up_to_date >= 0, na.rm = TRUE) +
sum(installed_pkg_df$GH_up_to_date >= 0, na.rm = TRUE)
# Is there anything to install or update?
if(n_missing + n_behind_CRAN + n_behind_GH > 0){
install_candidates <- installed_pkg_df[which(installed_pkg_df$installed == FALSE |
installed_pkg_df$CRAN_up_to_date == -1 |
installed_pkg_df$GH_up_to_date == -1),]
cat(" CRAN... ")
CRAN_df <- get_CRAN_data(install_candidates[install_candidates$on_CRAN,])
# Are there packages we need that are not found on CRAN? Try GitHub.
if(nrow(CRAN_df) < length(lib_list)){
cat("GitHub... ")
GH_df <- get_gh_data(install_candidates[!(install_candidates$package %in% CRAN_df$package),c("package","installed","installed_ver")])
} else GH_df <- data.frame()
cat("done.\n")
# Report installed and up to date dependencies.
if(n_uptodate_installed > 0){
cat("[deplearning] ",clisymbols::symbol$tick," ",n_uptodate_installed, " Installed and up to date.\n\n", sep = "")
cat("", paste0(installed_pkg_df$package[which(installed_pkg_df$installed == TRUE &
(installed_pkg_df$CRAN_up_to_date >= 0 |
installed_pkg_df$GH_up_to_date >= 0))], collapse = ", "),"\n\n")
}
# Report dependencies found on CRAN that are behind CRAN version.
if(n_behind_CRAN > 0){
cat("[deplearning] ",clisymbols::symbol$cross," ",n_behind_CRAN, " Installed but behind CRAN release.\n\n", sep = "")
print(as.data.frame(installed_pkg_df[which(installed_pkg_df$CRAN_up_to_date == -1),
c("package", "installed_ver","CRAN_ver")]),
row.names = FALSE)
cat("\n")
}
# Report Dependencies found on Github (not on CRAN), that are behind
# Github version.
if(n_behind_GH > 0){
cat("[deplearning] ",clisymbols::symbol$cross," ",n_behind_GH, " Installed but behind GitHub version.\n\n", sep = "")
print(as.data.frame(installed_pkg_df[which(installed_pkg_df$GH_up_to_date == -1),
c("GH_repository", "installed_ver","GH_ver")]),
row.names = FALSE)
cat("\n")
}
# Report uninstalled dependencies found on CRAN.
if(sum(!CRAN_df$installed) > 0){
cat("[deplearning] ", clisymbols::symbol$cross," ", sum(!CRAN_df$installed), " Missing CRAN packages.\n\n", sep = "")
cat(" ", paste0(CRAN_df$package[!CRAN_df$installed], collapse = ", "), "\n\n")
}
# Report uninstalled dependencies found on Github (not on CRAN).
if(sum(!GH_df$installed) > 0){
cat("[deplearning] ", clisymbols::symbol$cross," ", sum(!GH_df$installed), " Missing GitHub packages.\n\n", sep = "")
cat(" ", paste0(GH_df$repository[!GH_df$installed], collapse = ", "), "\n\n")
}
# Report dependencies that could not be found in a tracked repository.
# Tracked repositories are CRAN and GitHub.
lost_pkgs <- lib_list[!(lib_list %in% c(installed_pkg_df$package[installed_pkg_df$installed], CRAN_df$package, GH_df$package))]
if(length(lost_pkgs) > 0){
cat("[deplearning] ", clisymbols::symbol$cross," ", length(lost_pkgs), " Missing packages from untracked repositories.\n\n", sep = "")
cat(" ", paste0(lost_pkgs, collapse = ", "), "\n\n")
}
# If we found any packages that are uninstalled or are behind repository version:
# * Check that the installed R version is compatible with maximum
# R dependency. I.e. that we can install & update without updating R.
# If install & update is possible:
# * If GitHub packages need to be installed, check that devtools is intalled,
# If not, add it to CRAN dependencies and report this.
# * Report the set of all new recursive dependencies from CRAN and GitHub
# that would be installed along with detected dependencies.
# * Prompt user with choice to install & update missing and out of date
# dependencies. Install from CRAN, then GitHub as required.
if((nrow(GH_df) + nrow(CRAN_df)) > 0){
# Report minimum R version to install & update.
required_R_ver <- max_R_version(c(CRAN_df$R_ver, GH_df$R_ver))
current_R_ver <- paste0(version$major,".",version$minor)
cat("[deplearning] ",ifelse(compare_version(current_R_ver,required_R_ver) <= 0,
clisymbols::symbol$cross,
clisymbols::symbol$tick),
" Minimum R version to update & install is ", required_R_ver, ", you have ", current_R_ver,".\n",sep="")
if(compare_version(current_R_ver,required_R_ver) >= 0){
if(nrow(GH_df) > 0){
GH_df_recur_deps_CRAN <- unlist(purrr::map(GH_df$recur_dependencies, `[`, "CRAN_deps"))
GH_df_recur_deps_GH <- unlist(purrr::map(GH_df$recur_dependencies, `[`, "GH_deps"))
# If we might have to install Github dependencies, check for devtools and
# add it as a CRAN dependency if not installed.
if(!requireNamespace("devtools", quietly = TRUE)){
cat("[deplearning] ",clisymbols::symbol$info," devtools package is required to install from GitHub. Added to CRAN dependencies.", sep = "")
CRAN_df[nrow(CRAN_df)+1, "package"] <- "devtools"
CRAN_df[nrow(CRAN_df)+1, "recur_dependencies"] <- tools::package_dependencies(packages = "devtools",
recursive = TRUE)
}
}else{
GH_df_recur_deps_CRAN <- vector()
GH_df_recur_deps_GH <- vector()
}
if(nrow(CRAN_df) > 0){
CRAN_df_recur_deps <- unlist(CRAN_df$recur_dependencies)
}else{
CRAN_df_recur_deps <- vector()
}
# Deterimine missing recursive dependencies
# if else guards around deps vectors ensure they are not NULL and
# can be passed to below.
all_recur_CRAN_deps <- unique(c(GH_df_recur_deps_CRAN,
CRAN_df_recur_deps))
if(length(all_recur_CRAN_deps) > 0 ){
#Filter out installed recusrive dependencies.
missing_recur_CRAN_deps <- all_recur_CRAN_deps[!are_installed(all_recur_CRAN_deps)]
} else{
missing_recur_CRAN_deps <- list()
}
all_recur_GH_deps <- unique(GH_df_recur_deps_GH)
if(length(all_recur_GH_deps) > 0){
# Get just the package name so we can filter out installed recusrive
# dependencies.
GH_pack_names <- all_recur_GH_deps %>%
strsplit(split="/") %>%
purrr::map(`[`,2)
# Check the Github
missing_recur_GH_deps <- all_recur_GH_deps[!are_installed(GH_pack_names)]
}else{
missing_recur_GH_deps <- list()
}
all_missing_recur_deps <- c(missing_recur_CRAN_deps, missing_recur_GH_deps)
# Report missing recursive dependencies that will be installed if choice
# is made to install & update.
if(length(all_missing_recur_deps) > 0){
cat("[deplearning] ",clisymbols::symbol$info," Update & install will include ", length(all_missing_recur_deps)," new recursive dependencies.\n\n", sep = "")
cat(" ", paste0(all_missing_recur_deps, collapse = ", "), "\n\n")
}
# Prompt for choice to install and update
cat("[deplearning] Would you like to update & install old and missing dependencies?\n")
install_choice <- menu(c("Yes", "No"))
if(install_choice == 1){
#install CRAN deps
if(nrow(CRAN_df) > 0){
cat("[deplearning] Installing from CRAN.\n")
install.packages(CRAN_df$package)
}
if(nrow(GH_df) > 0){
cat("[deplearning] Installing from GitHub.\n")
if(requireNamespace("devtools")){
purrr::walk(GH_df$repository, ~devtools::install_github(.))
}
}
cat("[deplearning] Dependency check finished install & update. Check for errors/warnings.\n")
}else{
cat("[deplearning] Dependency check finished without install & update.\n")
}
}else{
# The R version is too old to update some dependencies
cat("[deplearning] R version needs to be updated to install & update dependencies.")
cat("[deplearning] Dependency check finished without install & update.\n")
}
}
}else{
# All dependencies present and and up to date.
cat(" done.\n")
cat("[deplearning] ", clisymbols::symbol$cross, " All available dependencies installed & up to date.\n\n", sep = "")
cat(" ",paste0(lib_list,collapse = ", "),"\n", sep="")
}
# Finally return the lists of packages found installed, and in tracked repositories
# for diagnostics or further processing. These may be empty dataframes.
invisible(list(install_status = installed_pkg_df, CRAN_packs = CRAN_df, GH_packs = GH_df))
}
# This helper appends metadata from CRAN and GitHub to locally installed dependencies.
get_installed_data <- function(installed_list){
CRAN_packs <- get_CRAN_pkgs()
installed_list$on_CRAN <-
purrr::map_lgl(installed_list$package, ~ . %in% CRAN_packs$Package )
installed_list$installed_ver <-
map_ifelse( .x = installed_list$package,
.p = installed_list$installed,
.f = ~packageDescription(., fields = "Version", drop = TRUE),
.e = NA) %>% unlist()
installed_list$CRAN_ver <-
map_ifelse(.x = installed_list$package,
.p = installed_list$on_CRAN,
.f = ~CRAN_packs$Version[CRAN_packs$Package == .],
.e = NA) %>% unlist()
installed_list$GH_acct <-
map_ifelse(.x = installed_list$package,
.p = !installed_list$on_CRAN & installed_list$installed,
.f = ~packageDescription(., fields = "GithubUsername", drop = TRUE),
.e = NA) %>% unlist()
installed_list$GH_packname <-
map_ifelse(.x = installed_list$package,
.p = !installed_list$on_CRAN & installed_list$installed,
.f = ~packageDescription(., fields = "GithubRepo", drop = TRUE),
.e = NA) %>% unlist()
installed_list$GH_repository <-
map_ifelse(.x = paste0(installed_list$GH_acct,"/",installed_list$GH_packname),
.p = !is.na(installed_list$GH_packname),
.f = ~.,
.e = NA) %>% unlist()
installed_list$GH_ver <-
map_ifelse(.x = installed_list$GH_repository,
.p = !is.na(installed_list$GH_packname),
.f = ~get_gh_DESCRIPTION_data(.)$version,
.e = NA) %>% unlist()
installed_list$CRAN_up_to_date <-
purrr::map2(.x = installed_list$installed_ver,
.y = installed_list$CRAN_ver,
.f = compare_version) %>% unlist()
installed_list$GH_up_to_date <-
purrr::map2( .x = installed_list$installed_ver,
.y = installed_list$GH_ver,
.f = compare_version) %>% unlist()
installed_list
}
MilesMcBain/deplearning documentation built on May 23, 2019, 3:12 p.m.
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#' Check R source dependencies.
#'
#' `depl_check` analyses R source for dependency references:
#' `library(<package>)`, `require(<package>)`, `<package>::func`,
#' `pload(<package>, <package>)`. The dependencies are then located in either the
#' local library, CRAN, or GitHub. Installed versions are compared with repository versions,
#' with CRAN taking precendence over GitHub (Even if a local package was installed from GitHub).
#'
#' A report is output to the console containing information about missing and out of date dependencies.
#' If there are any missing or out of date, a prompt is made to automatically update and install dependencies.
#'
#' @param source_path a file or directory path.
#'
#' @return A list of dataframes containing package metadata. Convenient for diagnostics or further processing.
#' @export
#'
#' @examples
#' \dontrun{
#' depl_check("~/repos/my_analysis")
#' depl_check("./report.Rmd")
#' }
#'
depl_check <- function(source_path = "."){
stopifnot(is.character(source_path))
cat("[deplearning] Starting dependency check.\n")
if(is_R_file(source_path)){
cat("[deplearning] Scanning file", source_path)
doc <- readLines(con = source_path)
lib_list <- find_doc_libs(doc)
}else{
cat("[deplearning] Searching path", source_path, "\n")
R_files <- dir(".", pattern = "\\.(rmd|r)$" , recursive = TRUE, ignore.case = TRUE)
if(length(R_files > 0)){
cat("[deplearning] Scanning", length(R_files), "R source files...")
lib_list <-
purrr::map(R_files, readLines) %>%
purrr::map(find_doc_libs) %>%
unlist() %>%
unique()
}else{
cat("[deplearning] Did not find any R source files in", source_path, ".\n")
return()
}
}
cat(" done.\n")
depl_check_run(lib_list)
}
#' Check R dependencies in the currently active Rstudio pane.
#'
#' See `depl_check()` for details.
#'
#' @return A list of dataframes containing package metadata. Convenient for diagnostics or further processing.
#' @export
depl_check_addin <- function(){
cat("[deplearning] Starting check run.\n")
cat("[deplearning] Scanning RStudio pane...")
lib_list <- find_doc_libs(rstudioapi::getActiveDocumentContext()$contents)
cat(" done.\n")
depl_check_run(lib_list)
}
# Subfunctuion of depl_check to allow the same body to be used for RStudio addin
# and file path version.
depl_check_run <- function(lib_list){
if(length(lib_list) == 0){
cat("[deplearning] found no dependencies in this code.\n")
return()
}
#remove base packages if present
lib_list <- lib_list[!lib_list %in% c("base","tools","utils")]
cat(sprintf("[deplearning] Found %i dependencies.\n", length(lib_list)))
pkg_install_status <-
tibble::tibble(
package = lib_list,
installed = are_installed(lib_list)
)
cat("[deplearning] Fetching remote data...")
installed_pkg_df <- get_installed_data(pkg_install_status)
n_behind_CRAN <- sum(installed_pkg_df$CRAN_up_to_date == -1, na.rm = TRUE)
n_behind_GH <- sum(installed_pkg_df$GH_up_to_date == -1, na.rm = TRUE)
n_missing <- sum(!pkg_install_status$installed)
n_uptodate_installed <-
sum(installed_pkg_df$CRAN_up_to_date >= 0, na.rm = TRUE) +
sum(installed_pkg_df$GH_up_to_date >= 0, na.rm = TRUE)
# Is there anything to install or update?
if(n_missing + n_behind_CRAN + n_behind_GH > 0){
install_candidates <- installed_pkg_df[which(installed_pkg_df$installed == FALSE |
installed_pkg_df$CRAN_up_to_date == -1 |
installed_pkg_df$GH_up_to_date == -1),]
cat(" CRAN... ")
CRAN_df <- get_CRAN_data(install_candidates[install_candidates$on_CRAN,])
# Are there packages we need that are not found on CRAN? Try GitHub.
if(nrow(CRAN_df) < length(lib_list)){
cat("GitHub... ")
GH_df <- get_gh_data(install_candidates[!(install_candidates$package %in% CRAN_df$package),c("package","installed","installed_ver")])
} else GH_df <- data.frame()
cat("done.\n")
# Report installed and up to date dependencies.
if(n_uptodate_installed > 0){
cat("[deplearning] ",clisymbols::symbol$tick," ",n_uptodate_installed, " Installed and up to date.\n\n", sep = "")
cat("", paste0(installed_pkg_df$package[which(installed_pkg_df$installed == TRUE &
(installed_pkg_df$CRAN_up_to_date >= 0 |
installed_pkg_df$GH_up_to_date >= 0))], collapse = ", "),"\n\n")
}
# Report dependencies found on CRAN that are behind CRAN version.
if(n_behind_CRAN > 0){
cat("[deplearning] ",clisymbols::symbol$cross," ",n_behind_CRAN, " Installed but behind CRAN release.\n\n", sep = "")
print(as.data.frame(installed_pkg_df[which(installed_pkg_df$CRAN_up_to_date == -1),
c("package", "installed_ver","CRAN_ver")]),
row.names = FALSE)
cat("\n")
}
# Report Dependencies found on Github (not on CRAN), that are behind
# Github version.
if(n_behind_GH > 0){
cat("[deplearning] ",clisymbols::symbol$cross," ",n_behind_GH, " Installed but behind GitHub version.\n\n", sep = "")
print(as.data.frame(installed_pkg_df[which(installed_pkg_df$GH_up_to_date == -1),
c("GH_repository", "installed_ver","GH_ver")]),
row.names = FALSE)
cat("\n")
}
# Report uninstalled dependencies found on CRAN.
if(sum(!CRAN_df$installed) > 0){
cat("[deplearning] ", clisymbols::symbol$cross," ", sum(!CRAN_df$installed), " Missing CRAN packages.\n\n", sep = "")
cat(" ", paste0(CRAN_df$package[!CRAN_df$installed], collapse = ", "), "\n\n")
}
# Report uninstalled dependencies found on Github (not on CRAN).
if(sum(!GH_df$installed) > 0){
cat("[deplearning] ", clisymbols::symbol$cross," ", sum(!GH_df$installed), " Missing GitHub packages.\n\n", sep = "")
cat(" ", paste0(GH_df$repository[!GH_df$installed], collapse = ", "), "\n\n")
}
# Report dependencies that could not be found in a tracked repository.
# Tracked repositories are CRAN and GitHub.
lost_pkgs <- lib_list[!(lib_list %in% c(installed_pkg_df$package[installed_pkg_df$installed], CRAN_df$package, GH_df$package))]
if(length(lost_pkgs) > 0){
cat("[deplearning] ", clisymbols::symbol$cross," ", length(lost_pkgs), " Missing packages from untracked repositories.\n\n", sep = "")
cat(" ", paste0(lost_pkgs, collapse = ", "), "\n\n")
}
# If we found any packages that are uninstalled or are behind repository version:
# * Check that the installed R version is compatible with maximum
# R dependency. I.e. that we can install & update without updating R.
# If install & update is possible:
# * If GitHub packages need to be installed, check that devtools is intalled,
# If not, add it to CRAN dependencies and report this.
# * Report the set of all new recursive dependencies from CRAN and GitHub
# that would be installed along with detected dependencies.
# * Prompt user with choice to install & update missing and out of date
# dependencies. Install from CRAN, then GitHub as required.
if((nrow(GH_df) + nrow(CRAN_df)) > 0){
# Report minimum R version to install & update.
required_R_ver <- max_R_version(c(CRAN_df$R_ver, GH_df$R_ver))
current_R_ver <- paste0(version$major,".",version$minor)
cat("[deplearning] ",ifelse(compare_version(current_R_ver,required_R_ver) <= 0,
clisymbols::symbol$cross,
clisymbols::symbol$tick),
" Minimum R version to update & install is ", required_R_ver, ", you have ", current_R_ver,".\n",sep="")
if(compare_version(current_R_ver,required_R_ver) >= 0){
if(nrow(GH_df) > 0){
GH_df_recur_deps_CRAN <- unlist(purrr::map(GH_df$recur_dependencies, `[`, "CRAN_deps"))
GH_df_recur_deps_GH <- unlist(purrr::map(GH_df$recur_dependencies, `[`, "GH_deps"))
# If we might have to install Github dependencies, check for devtools and
# add it as a CRAN dependency if not installed.
if(!requireNamespace("devtools", quietly = TRUE)){
cat("[deplearning] ",clisymbols::symbol$info," devtools package is required to install from GitHub. Added to CRAN dependencies.", sep = "")
CRAN_df[nrow(CRAN_df)+1, "package"] <- "devtools"
CRAN_df[nrow(CRAN_df)+1, "recur_dependencies"] <- tools::package_dependencies(packages = "devtools",
recursive = TRUE)
}
}else{
GH_df_recur_deps_CRAN <- vector()
GH_df_recur_deps_GH <- vector()
}
if(nrow(CRAN_df) > 0){
CRAN_df_recur_deps <- unlist(CRAN_df$recur_dependencies)
}else{
CRAN_df_recur_deps <- vector()
}
# Deterimine missing recursive dependencies
# if else guards around deps vectors ensure they are not NULL and
# can be passed to below.
all_recur_CRAN_deps <- unique(c(GH_df_recur_deps_CRAN,
CRAN_df_recur_deps))
if(length(all_recur_CRAN_deps) > 0 ){
#Filter out installed recusrive dependencies.
missing_recur_CRAN_deps <- all_recur_CRAN_deps[!are_installed(all_recur_CRAN_deps)]
} else{
missing_recur_CRAN_deps <- list()
}
all_recur_GH_deps <- unique(GH_df_recur_deps_GH)
if(length(all_recur_GH_deps) > 0){
# Get just the package name so we can filter out installed recusrive
# dependencies.
GH_pack_names <- all_recur_GH_deps %>%
strsplit(split="/") %>%
purrr::map(`[`,2)
# Check the Github
missing_recur_GH_deps <- all_recur_GH_deps[!are_installed(GH_pack_names)]
}else{
missing_recur_GH_deps <- list()
}
all_missing_recur_deps <- c(missing_recur_CRAN_deps, missing_recur_GH_deps)
# Report missing recursive dependencies that will be installed if choice
# is made to install & update.
if(length(all_missing_recur_deps) > 0){
cat("[deplearning] ",clisymbols::symbol$info," Update & install will include ", length(all_missing_recur_deps)," new recursive dependencies.\n\n", sep = "")
cat(" ", paste0(all_missing_recur_deps, collapse = ", "), "\n\n")
}
# Prompt for choice to install and update
cat("[deplearning] Would you like to update & install old and missing dependencies?\n")
install_choice <- menu(c("Yes", "No"))
if(install_choice == 1){
#install CRAN deps
if(nrow(CRAN_df) > 0){
cat("[deplearning] Installing from CRAN.\n")
install.packages(CRAN_df$package)
}
if(nrow(GH_df) > 0){
cat("[deplearning] Installing from GitHub.\n")
if(requireNamespace("devtools")){
purrr::walk(GH_df$repository, ~devtools::install_github(.))
}
}
cat("[deplearning] Dependency check finished install & update. Check for errors/warnings.\n")
}else{
cat("[deplearning] Dependency check finished without install & update.\n")
}
}else{
# The R version is too old to update some dependencies
cat("[deplearning] R version needs to be updated to install & update dependencies.")
cat("[deplearning] Dependency check finished without install & update.\n")
}
}
}else{
# All dependencies present and and up to date.
cat(" done.\n")
cat("[deplearning] ", clisymbols::symbol$cross, " All available dependencies installed & up to date.\n\n", sep = "")
cat(" ",paste0(lib_list,collapse = ", "),"\n", sep="")
}
# Finally return the lists of packages found installed, and in tracked repositories
# for diagnostics or further processing. These may be empty dataframes.
invisible(list(install_status = installed_pkg_df, CRAN_packs = CRAN_df, GH_packs = GH_df))
}
# This helper appends metadata from CRAN and GitHub to locally installed dependencies.
get_installed_data <- function(installed_list){
CRAN_packs <- get_CRAN_pkgs()
installed_list$on_CRAN <-
purrr::map_lgl(installed_list$package, ~ . %in% CRAN_packs$Package )
installed_list$installed_ver <-
map_ifelse( .x = installed_list$package,
.p = installed_list$installed,
.f = ~packageDescription(., fields = "Version", drop = TRUE),
.e = NA) %>% unlist()
installed_list$CRAN_ver <-
map_ifelse(.x = installed_list$package,
.p = installed_list$on_CRAN,
.f = ~CRAN_packs$Version[CRAN_packs$Package == .],
.e = NA) %>% unlist()
installed_list$GH_acct <-
map_ifelse(.x = installed_list$package,
.p = !installed_list$on_CRAN & installed_list$installed,
.f = ~packageDescription(., fields = "GithubUsername", drop = TRUE),
.e = NA) %>% unlist()
installed_list$GH_packname <-
map_ifelse(.x = installed_list$package,
.p = !installed_list$on_CRAN & installed_list$installed,
.f = ~packageDescription(., fields = "GithubRepo", drop = TRUE),
.e = NA) %>% unlist()
installed_list$GH_repository <-
map_ifelse(.x = paste0(installed_list$GH_acct,"/",installed_list$GH_packname),
.p = !is.na(installed_list$GH_packname),
.f = ~.,
.e = NA) %>% unlist()
installed_list$GH_ver <-
map_ifelse(.x = installed_list$GH_repository,
.p = !is.na(installed_list$GH_packname),
.f = ~get_gh_DESCRIPTION_data(.)$version,
.e = NA) %>% unlist()
installed_list$CRAN_up_to_date <-
purrr::map2(.x = installed_list$installed_ver,
.y = installed_list$CRAN_ver,
.f = compare_version) %>% unlist()
installed_list$GH_up_to_date <-
purrr::map2( .x = installed_list$installed_ver,
.y = installed_list$GH_ver,
.f = compare_version) %>% unlist()
installed_list
}
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